Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments.

Phased DNA methylation states within bisulfite sequencing reads are valuable source of information that can be used to estimate epigenetic diversity across cells as well as epigenomic instability in individual cells. Various measures capturing the heterogeneity of DNA methylation states have been proposed for a decade. However, in routine analyses on DNA methylation, this heterogeneity is often ignored by computing average methylation levels at CpG sites, even though such information exists in bisulfite sequencing data in the form of phased methylation states, or methylation patterns. In this study, to facilitate the application of the DNA methylation heterogeneity measures in downstream epigenomic analyses, we present a Rust-based, extremely fast and lightweight bioinformatics toolkit called Metheor. As the analysis of DNA methylation heterogeneity requires the examination of pairs or groups of CpGs throughout the genome, existing softwares suffer from high computational burden, which almost make a large-scale DNA methylation heterogeneity studies intractable for researchers with limited resources. In this study, we benchmark the performance of Metheor against existing code implementations for DNA methylation heterogeneity measures in three different scenarios of simulated bisulfite sequencing datasets. Metheor was shown to dramatically reduce the execution time up to 300-fold and memory footprint up to 60-fold, while producing identical results with the original implementation, thereby facilitating a large-scale study of DNA methylation heterogeneity profiles. To demonstrate the utility of the low computational burden of Metheor, we show that the methylation heterogeneity profiles of 928 cancer cell lines can be computed with standard computing resources. With those profiles, we reveal the association between DNA methylation heterogeneity and various omics features. Source code for Metheor is at https://github.com/dohlee/metheor and is freely available under the GPL-3.0 license.

Learning the histone codes with large genomic windows and three-dimensional chromatin interactions using transformer.

The quantitative characterization of the transcriptional control by histone modifications has been challenged by many computational studies, but most of them only focus on narrow and linear genomic regions around promoters, leaving a room for improvement. We present Chromoformer, a transformer-based, three-dimensional chromatin conformation-aware deep learning architecture that achieves the state-of-the-art performance in the quantitative deciphering of the histone codes in gene regulation. The core essence of Chromoformer architecture lies in the three variants of attention operation, each specialized to model individual hierarchy of transcriptional regulation involving from core promoters to distal elements in contact with promoters through three-dimensional chromatin interactions. In-depth interpretation of Chromoformer reveals that it adaptively utilizes the long-range dependencies between histone modifications associated with transcription initiation and elongation. We also show that the quantitative kinetics of transcription factories and Polycomb group bodies can be captured by Chromoformer. Together, our study highlights the great advantage of attention-based deep modeling of complex interactions in epigenomes.

Direct-Writable and Thermally One-Step Curable "Water-Stained" Epoxy Composite Inks.

In this study, a simple method for preparing direct-writable and thermally one-step curable epoxy composite inks was proposed. Specifically, colloidal inks containing a mixture of ordinary epoxy resin and anhydride-type hardener with the suspended alumina microplates, as exemplary fillers, are "stained" with small amounts of water. This increases the elasticity of the ink via the interparticle capillary attraction and promotes curing of the epoxy matrix in low-temperature ranges, causing the three-dimensional (3D) printed ink to avoid structural disruption during one-step thermal curing without the tedious pre-curing step. The proposed mechanisms for the shape retention of thermally cured water-stained inks were discussed with thorough analyses using shear rheometry, DSC, FTIR, and SEM. Results of the computer-vision numerical analysis of the SEM images reveal that the particles in water-stained inks are oriented more in the vertical direction than those in water-free samples, corroborating the proposed mechanisms. The suggested concept is extremely simple and does not require any additional cost to the one required for the preparation of the common epoxy-filler composites, which is thus expected to be well-exploited in various applications where 3D printing of epoxy-based formulations is necessary.

A pickering emulsion stabilized by chlorella microalgae as an eco-friendly extrusion-based 3D printing ink processable under ambient conditions.

Three-dimensional (3D) printing technology is actively utilized in various industrial fields because it facilitates effective and customizable fabrication of complex structures. An important processing route for 3D printing is the extrusion of inks in the form of colloidal suspensions or emulsions, which has recently attracted considerable attention because it allows for selection of a wide range of printing materials and is operable under ambient processing conditions. Herein, we investigate the 3D printability of complex fluids containing chlorella microalgae as an eco-friendly material for 3D printing. Two possible ink types are considered: aqueous chlorella suspensions and emulsions of oil and water mixtures. While the aqueous chlorella suspensions at high particle loading display the 3D-printable rheological properties such as high yield stress and good shape retention, the final structures after extruding and drying the suspensions under ambient conditions show a significant number of macroscopic defects, limiting their practical application. In contrast, the 3D structures produced from the oil-in-water Pickering emulsions stabilized by chlorella microalgae, which are amphiphilic and active at the oil-water interface, show significantly reduced defect formation. Addition of a fast-evaporable oil phase, hexane, is crucial in the mechanisms of enhanced cementation between the individual microalgae via increased inter-particle packing, capillary attraction, and hydrophobic interaction. Furthermore, addition of solid paraffin wax, which is crystalline but well-soluble in the hydrocarbon oil phase under ambient conditions, completely eliminates the undesirable defect formation via enhanced inter-particle binding, while maintaining the overall rheological properties of the emulsion. The optimal formulation of the Pickering emulsion is finally employed to produce a 3D scaffold of satisfactory structural integrity, suggesting that the chlorella-based ink, in the form of an emulsion, has potential as an eco-friendly 3D printing ink processable under ambient conditions.

Role of electrostatic interactions in the adsorption of dye molecules by Ti3C2-MXenes.

MXenes, a new class of 2D materials, have recently attracted increasing attention as promising adsorbents for environmental remediation. It has been previously demonstrated that MXenes can successfully capture selected organic dyes from aqueous media; however, to date, the adsorption performance of MXenes for a wide variety of dyes in simulated real-life aquatic environments other than clean laboratory deionized (DI) water has not been systematically investigated. In this study, we systematically investigated the adsorption performance of delaminated Ti3C2-MXenes for six different organic dyes in aquatic media at different pH levels and ionic strengths. Our results strongly suggest the importance of the electrostatic interactions between the ionizable functional groups of MXenes and dyes for removal efficiency. The electrostatic repulsions between negatively charged MXenes and certain anionic dyes reduced the removal efficiencies of MXenes for these dyes in DI water; however, the presence of divalent cations significantly improved the removal efficiencies, possibly owing to the charge screening effects and like-charge attractions mediated by cation binding to the functionalities of dyes and MXenes. These results provide a rational strategy for optimizing the conditions for efficient removal of different types of organic dyes using MXenes.

Bulk Nanoencapsulation of Phase Change Materials (PCMs) via Spontaneous Spreading of a UV-Curable Prepolymer.

Phase change materials (PCMs) have received considerable attention for various latent heat storage systems for efficient thermal energy utilization. Herein, a facile and fast method for the bulk nanoencapsulation of organic PCMs is proposed, based on the thermodynamically spontaneous spreading phenomenon of three immiscible liquid phases. In this approach, a complete engulfing of PCM nanodroplets (core phase) by immiscible prepolymer droplets (coating phase), both of which are bulk-dispersed in another immiscible medium (continuous phase), is thermodynamically driven by the relation between the surface energies of the core, coating, and continuous phases. To demonstrate the proposed method, melted n-docosane (PCM, core phase) nanodroplets are completely engulfed within a couple of minutes by immiscible polyethylene glycol diacrylate (PEGDA, coating phase) in an aqueous poly(vinyl alcohol) solution (continuous phase), and the PEGDA layer quickly cross-linked upon UV irradiation to form a rigid shell protecting the PCM core. As-produced PCM nanocapsules display promising heat storage and release performances as well as high durability in repeated heating-cooling cycles in both dry and wet states. The proposed process may serve as a useful platform for bulk production of PCM nanocapsules with various core and shell compositions in a facile, fast, and scalable way.

Yield Stress Enhancement of a Ternary Colloidal Suspension via the Addition of Minute Amounts of Sodium Alginate to the Interparticle Capillary Bridges.

Capillary suspensions are ternary solid-liquid-liquid systems produced via the addition of a small amount of secondary fluid to the bulk fluid that contained the dispersed solid particles. The secondary fluid could exert strong capillary forces between the particles and dramatically change the rheological properties of the suspension. So far, research has focused on capillary suspensions that consist of additive-free fluids, whereas capillary suspensions with additives, particularly those of large molecular weight that are highly relevant for industrial purposes, have been relatively less studied. In this study, we performed a systematic analysis of the properties of capillary suspensions that consist of paraffin oil (bulk phase), water (secondary phase), and α-Al2O3 microparticles (particle phase), in which the aqueous secondary phase contained an important eco-friendly polymeric binder, sodium alginate (SA). It was determined that the yield stress of the suspension increased significantly with the increase in the SA content in the aqueous secondary phase, which was attributed to the synergistic effect of the capillary force and hydrogen bonding force that may be related to the increase in the number of capillary bridges. The amounts of SA used to induce a significant change in the yield stress in this study were very small (<0.02% of the total sample volume). The addition of Ca2+ ions to the SA-containing secondary phase further increased the yield stress with possible gelation of the SA chains-in the presence of excess Ca2+ ions, however, the yield stress decreased because of the microscopic phase separation that occurred in the aqueous secondary phase. The microstructures of the sintered porous materials that were produced by using capillary suspensions as precursors were qualitatively well correlated to the rheological behavior of the precursor suspensions, suggesting a new method for the subtle control of the microstructures of porous materials using the addition of minute amounts of polymeric additives.

A Systematic Investigation on the Properties of Silica Nanoparticles "Multipoint"-Grafted with Poly(2-acrylamido-2-methylpropanesulfonate-co-acrylic Acid) in Extreme Salinity Brines and Brine-Oil Interfaces.

Nanoparticles (NPs) may have great potential for various subsurface applications, including oil and gas recovery, reservoir imaging, and environmental remediation. One of the important challenges for these downhole applications is to achieve colloidal stability in subsurface media at high salinity and high temperature. It has been previously shown that several functional NPs "multipoint"-grafted with anionic poly(2-acrylamido-2-methyl-1-propanesulfonate-co-acrylic acid; AMPS-co-AA) exhibited remarkable colloidal stabilities in specific environments mimicking the harsh subsurface aquatic media, such as the American Petroleum Institute (API) brine. However, many important properties of such particles, other than the colloidal stabilities, must be studied in a more systematic fashion for a wide range of salt concentrations (Cs). Herein, we investigate various properties of the silica (SiO2) NPs multipoint-grafted with poly(AMPS-co-AA), SiO2-g-poly(AMPS-co-AA), in NaCl and CaCl2 solutions across a range of salinities. The brush behavior of the grafted random copolymers was investigated in both salt solutions from salt-free conditions up to extreme salinities. The particles displayed brine-oil interfacial activity with increasing Cs, stabilizing oil-in-brine emulsions as Pickering emulsifiers. A high internal phase emulsion (HIPE) with an internal oil phase of up to 80 vol % could be formed in CaCl2 solutions at high Cs, which exhibited gel-like behaviors.

Polyelectrolyte-grafted Ti3C2-MXenes stable in extreme salinity aquatic conditions for remediation of contaminated subsurface environments.

MXenes, an emerging class of two-dimensional materials, are recently gaining significant attention for numerous environmental applications owing to their superior hydrophilicity and unique surface functionalities, which are suitable for adsorptive removal of various aqueous contaminants. However, it has recently been shown that MXenes have poor colloidal stability in both synthetic or natural waters containing small amounts of salt ions, which will limit the potential uses of MXenes in remediation of subsurface environments that might sometimes contain considerable amounts of salt ions, and other relevant environmental applications. Herein, we develop Ti3C2-MXenes grafted with highly salt-resistant polyelectrolytes (PEs), MXene-g-PEs, which are colloidally stable in extreme salinity aquatic environments and have low adsorption to soil mineral substrates. The MXenes grafted with zwitterionic PEs are found to have superior mobility properties to those with anionic PEs, which are attributed to the anti-PE behavior of the grafted polymer brushes. The MXene-g-(zwitterionic) PEs show long-term colloidal stability over 6 months in American Petroleum Institute (API) brine with extreme salinity (ionic strength of 2 M with 182.2 mM Ca2+), and little adsorption (0.5 mg m-2) against α-alumina surfaces (2.3 m2 g-1). Furthermore, the MXene-g-PEs retained the excellent adsorption capacity for methylene blue as a model aqueous organic pollutant. The results suggest the great potential of the MXene-g-PEs as an aqueous pollutant scavenger for various environmental applications including the combined ex situ/in situ remediation, and other relevant subsurface applications.